Accredited official statistics

Quarterly epidemiological commentary: mandatory Gram-negative bacteraemia, MRSA, MSSA and C. difficile infections (data up to April to June 2022)

Updated 6 November 2024

Applies to England

UK Health Security Agency and this report

Beginning in April 2021, the UK Health Security Agency (UKHSA) was created and is responsible for protecting every member of every community from the effect of infectious diseases, chemical, biological, radiological, and nuclear incidents and other health threats. We provide intellectual, scientific, and operational leadership at national and local level, as well as on the global stage, to make the nation’s health secure.

The agency replaces Public Health England (PHE) and is an executive agency of the Department of Health and Social Care (DHSC). The transition to UKHSA included the integration of both staff and systems. Accordingly, the systems and processes responsible for the publication of the previous annual epidemiological commentaries were incorporated into UKHSA. The same methods of data capture, analysis and dissemination have been employed in the production of this report.

Data included in this quarterly epidemiological commentary

This document contains quarterly, national-level epidemiological commentaries for meticillin resistant Staphylococcus aureus (MRSA), meticillin susceptible Staphylococcus aureus (MSSA), Escherichia coli (E. coli), Klebsiella spp. and Pseudomonas aeruginosa (P. aeruginosa) bacteraemia and Clostridioides difficile infection (CDI). These include analyses on counts and incidence rates of all reported, hospital-onset (previously referred to as trust-apportioned) and community-onset (previously referred to as non trust-apportioned) cases of MRSA, MSSA, E. coli, Klebsiella spp. and P. aeruginosa bacteraemia and CDI. All data tables associated with this report are included in an OpenDocument spreadsheet.

Revisions to data included are covered by a data-specific revisions and correction policy.

Citation to UK Health Security Agency (UKHSA), healthcare associated infections (HCAI) and antimicrobial resistance (AMR) division is required, if these data are used for publication elsewhere, using the content below.

Citation: UK Health Security Agency. Quarterly epidemiology commentary: mandatory MRSA, MSSA and Gram-negative bacteraemia and C. difficile infection in England (up to April to June 2022) London: UK Health Security Agency, October 2022.

COVID-19 and these data

The coronavirus (COVID-19) pandemic appears to have affected the number of cases of both bacteraemia and CDI observed during the period March 2020 to June 2022. In general, counts of all reported bloodstream infections (BSI) and CDI cases covered in this report during the financial year April 2020 to March 2021 were lower than would be expected, while counts of hospital-onset Klebsiella spp. and P. aeruginosa cases increased and exceeded previous counts of cases observed in this setting. Most of the declines in bacteraemia and CDI cases initially observed during the COVID-19 pandemic occurred within community-onset cases.

During the second and third wave, covering quarters October to December 2020 to January to March 2022, the overall number of infections increased after the decline in the first wave for all organisms, except for E. coli and MRSA bacteraemias which are still at a lower rate than pre-pandemic. Incidence of hospital-onset CDI and Klebsiella spp. and P. aeruginosa bacteraemias were increased compared to the pre-pandemic period.

For the most recent quarter, April to June 2022, all Gram-negative bacteraemias and MSSA are at the same rate or exceeding levels observed since the start of surveillance. The exception is MRSA bacteraemia, which has stabilised and appears to be on a downward trend. A gradual incline in CDI cases has been observed since the pandemic, in both all reported and hospital cases.

Analysis of voluntary laboratory surveillance data also showed a reduction (albeit to different extents) in cases of the majority of other bloodstream infections not covered by the mandatory surveillance during this period. As the voluntary laboratory surveillance shows similar trends to the mandatory surveillance scheme, these changes do not appear to be a specific ascertainment problem in the mandatory programme.

In response to the pandemic, elective procedures in hospitals were initially cancelled or delayed, although some activity resumed between COVID-19 waves. As a result, the number of occupied overnight beds – the denominator used for hospital-onset infection rates – was much lower than would otherwise be expected during these periods, particularly for financial year April 2020 to March 2021, with some increase in financial year April 2021 to March 2022, albeit remaining lower than in financial year April 2019 to March 2020. Therefore, in some instances, increased incidence rates of hospital-onset infection have been reported, despite a decrease in the counts of infections.

This report covers data up to the end of June 2022, encompassing the first, second and third COVID-19 wave in England. The full effect of the active pandemic on healthcare-associated infections cannot yet be determined and it is impossible to estimate with any certainty at present if HCAI trends will return to those seen pre-COVID-19. If changes in patient populations and NHS practice remain long-term, then the HCAI trends will need to be reassessed with consideration of these changes.

Further information

This publication forms part of the range of National Statistics outputs routinely published by UKHSA which include monthly and annual reports on the mandatory surveillance of MRSA, MSSA and E. coli, Klebsiella spp. and P. aeruginosa bacteraemia and CDI.

Annual report output

Further epidemiological analyses by financial year can be found in UKHSA’s annual epidemiological commentary.

Monthly report outputs

The following reports are produced by UKHSA monthly.

MRSA bacteraemia – counts of all reported, hospital-onset cases, community-onset cases, healthcare associated and community associated MRSA bacteraemia by organisation.

MSSA bacteraemia – counts of all reported, hospital-onset cases, community-onset cases, healthcare associated and community associated MSSA bacteraemia by organisation.

E. coli bacteraemia – counts of all reported, hospital-onset cases, community-onset cases, healthcare associated and community associated E. coli bacteraemia by organisation.

Klebsiella spp. bacteraemia – counts of all reported, hospital-onset cases, community-onset cases, healthcare associated and community associated Klebsiella spp. bacteraemia by organisation.

P. aeruginosa bacteraemia – counts of all reported, hospital-onset cases, community-onset cases, healthcare associated and community associated P. aeruginosa bacteraemia by organisation.

CDI – counts of all reported, hospital-onset cases, community-onset cases, healthcare associated and community associated CDI by organisation.

Data for this report was extracted from UKHSA’s HCAI data capture system (DCS) on 23 August 2022.

Epidemiological analyses of Gram-negative bacteraemia data

E. coli bacteraemia

The incidence rate of all reported E. coli bacteraemia increased each financial year between the initiation of the mandatory surveillance of E. coli bacteraemia in July 2011 and the start of the COVID-19 pandemic (January to March 2020, Figure 1a). This increase was primarily caused by community-onset cases (see Table S1 in the accompanying data tables). The number and incidence rates of all reported and community-onset cases declined after the start of the pandemic, but remain higher than observed at the start of E. coli surveillance (Figure 1a). In contrast, the incidence rate of hospital-onset cases remained relatively stable during the same period, except for a sharp reduction (20.7 cases per 100,000 bed days) observed in April to June 2021 (Figure 1b). This is followed by a steady return to pre-pandemic rates, however remaining lower than the start of E. coli surveillance.

Comparing quarters July to September 2011 and April to June 2022, the count and the incidence rate of all reported cases of E. coli bacteraemia increased by 15.9% from 8,275 cases to 9,593 and from 61.8 to 68.2 cases per 100,000 population, respectively. Similarly, over the same period, the count of community-onset cases increased by 22.8% from 6,279 to 7,710, while the incidence rate increased by 16.9% from 46.9 to 54.8 cases per 100,000 population. Concurrently, the count of hospital-onset cases decreased by 5.7% from 1,996 to 1,883 cases. This corresponded to a decrease in the incidence rate of hospital-onset cases by 8.1% from 23.6 per 100,000 bed-days to 21.7 per 100,000 bed-days.

When comparing the most recent quarter (April to June 2022) to the same period in the previous year (April to June 2021) there was a 1.4% decrease in both the count and incidence rate of all reported cases from 9,733 to 9,593 and 69.2 to 68.2 per 100,000 population, respectively (Figure 1a). Over the same time period, community-onset E. coli bacteraemia cases decreased by 5.0% from 8,118 to 7,710, with the community-onset incidence rate decreasing by the same percentage (5.0% from 57.7 to 54.8 per 100,000 population, Table S1 in the accompanying data tables.

In April to June 2022, hospital-onset E. coli bacteraemia cases increased by 16.6% from 1,615 to 1,883 compared to April to June 2021 (Figure 1b). However, over the same period the incidence rate increased by a lesser amount, 4.7% from 20.7 to 21.7 per 100,000 bed-days. It is important that these figures are interpreted with caution. Fluctuations in the level of hospital admissions during the pandemic has affected the total count of occupied overnight patient bed-days since 2021, which is used as the denominator for the calculation of hospital-onset rates. Overnight bed-days were 56.0% higher in April to June 2022 when compared to the same quarter in 2020. There has been a slow return to more typical counts of overnight bed-days in the current quarter (April to June 2022), which is 11.3% higher than the same quarter in 2021. The relatively slower increase in incidence rates than counts of hospital-onset E. coli bacteraemia is due to a steady return to the typical number of overnight bed-days in April to June 2022, compared to the unusually low levels in April to June 2020. While there has been a steady increase in hospital admissions, this is happening at a greater magnitude than the increase in cases, resulting in a decline in incidence rate being observed.

When comparing the most recent quarter (April to June 2022) with April to June 2019, which is a more typical period for hospital activity and healthcare seeking behaviours than during the COVID-19 pandemic, there is a 12.5% decrease in total cases from 10,965 to 9,593, with a corresponding decrease of 12.7% in the incidence rate from 78.1 to 68.2 cases per 100,000 population (Figure 1a). Community-onset cases decreased by 14.8% from 9,044 to 7,710. Similarly, the incidence rate of community-onset cases also declined by 14.9% from 64.4 to 54.8 cases per 100,000 population. Finally, the total numbers of hospital-onset cases decreased by 2.0% compared to the same period from 1,921 to 1,883, while the hospital-onset incidence rate fell by 2.6% from 22.2 to 21.7 cases per 100,000 bed-days (Figure 1b). These highlight the decline in reports of E. coli bacteraemia cases since the start of the COVID-19 pandemic.

There appears to be a seasonality to the incidence of all-reported E. coli bacteraemia cases, with the highest rates observed between July to September of each year, although care is required in interpreting data for financial years April 2020 to March 2021 and April 2021 to March 2022 due to the reduction in cases and hospital activity during the pandemic.

Figure 1a. Quarterly rates of all reported E. coli bacteraemia: July to September 2011, to April to June 2022

Figure 1b. Quarterly rates of hospital-onset E. coli bacteraemia: July to September 2011, to April to June 2022

Since April 2020, community-onset cases E. coli bacteraemia cases have been further categorised based on a patient’s previous discharge (or not) from the same reporting acute trust within 28 days.

Cases with no previous discharge within 28 days prior to the current episode start date was recorded, community-onset, community-associated (COCA) cases, accounted for the majority of reported community-onset E. coli bacteraemia, between April to June 2020 and April to June 2022. While there have been some fluctuations, the proportion of COCA cases has remained similar at around two-thirds of all cases.

Although the distribution of cases by these categories remained broadly stable, when comparing the number of COHA cases from the current quarter (April to June 2022) to the same quarter in 2021 (April to June 2021), COHA cases decreased from 15.0% to 14.3% as did hospital-onset healthcare associated (HOHA) cases from 16.6% to 19.6% of cases. COCA cases, on the other hand, decreased from 67.9% to 65.9%.

Figure 1c. Count of E. coli bacteraemia cases by prior trust exposure: April to June 2020, to April to June 2022

Klebsiella spp. bacteraemia

Between April to June 2017 and April to June 2022, there was a 15.4% increase in the count of all reported Klebsiella spp. bacteraemia cases from 2,348 to 2,709 and a 13.8% increase in the incidence rate from 16.9 to 19.3 cases per 100,000 population (Figure 2a).

The count of community-onset cases increased by 10.0% from 1,678 to 1,845 cases, between the April to June 2017 and April to June 2022 quarters, the incidence rate also increased by 8.4% from 12.1 to 13.1 cases per 100,000 population. Over the same period, the count of hospital-onset cases increased by 29.0% from 670 to 864 cases and the incidence rate increased by 28.2% from 7.8 to 9.9 cases per 100,000 bed-days (Figure 2b, Table S2 in the accompanying data tables). Counts and rates of hospital-onset Klebsiella spp. had an observed peak between the July to September 2020 and January to March 2021 quarters which were during the COVID-19 pandemic. Both counts and rates of hospital-onset cases increased to levels which were the highest observed since the inception of mandatory Klebsiella spp. surveillance. The incidence rate of hospital-onset cases peaked at 15.5 cases per 100,000 bed-days during the January to March 2021 quarter. The specific causes of this increase are still being investigated, but we do know these trends coincided with increased incidence of COVID-19 (1).

In the most recent quarter (April to June 2022), the number of hospital-onset Klebsiella spp. bacteraemia cases increased by 11.2% from 777 to 864 but there was no change in the incidence rate per 100,000 population, when compared with the same quarter in the previous financial year (April to June 2021). Compared to the same period in 2019 (April to June 2019) a more typical year prior to the pandemic, the counts and the incidence rate of hospital-onset cases increased by 14.4% and 13.8%, respectively. The number of all reported cases and incident rate in the current quarter compared to the same period in 2019 (April to June 2019) increased by 6.2% from 2,590 to 2,709 cases and from 18.4 to 19.3 per 100,000 population, respectively (Figure 2a, Table S2 in the accompanying data tables). The number of community-onset Klebsiella spp. cases increased by 2.7% (absolute change 1,797 to 1,845) and the infection rate increased from 12.9 to 13.1 per 100,000 population (Table S2 in the accompanying data tables).

During the April to June 2022 quarter, 71.9% (1,947 of 2,709) of all reported Klebsiella spp. bacteraemia were caused by Klebsiella pneumoniae, similar to the same quarter in the previous year (71.7%, April to June 2021). In April to June 2022, 17.5% of cases identified as Klebsiella oxytoca (473 of 2,709), a decrease from the 18.4% reported in April to June 2021.

The incidence rate of the majority of Klebsiella species increased at roughly the same pace (Figure 2a, Table S2 in the accompanying data tables). The exception to this was the incidence rate of K. oxytoca, which increased within hospital-onset cases around the start of the pandemic and subsequently stabilised at between 1.9 to 2.1 per 100,000 bed days.

There is evidence of seasonality in the trend of all reported Klebsiella spp. bacteraemia cases, with the highest incidence rates normally observed in July to September of each year. However, it is important to evaluate financial year April 2020 to March 2021 and April 2021 to March 2022 with caution.

Figure 2a. Quarterly rates of all reported Klebsiella spp. bacteraemia by species: April to June 2017, to April to June 2022

Figure 2b. Quarterly rates of hospital-onset Klebsiella spp. bacteraemia: April to June 2017, to April to June 2022

Like E. coli bacteraemia, between April to June 2020 and April to June 2022, COCA cases made up the largest percentage of all Klebsiella spp. bacteraemia, accounting for around half of all cases (Figure 2c).

HOHA cases peaked at 39.7% in January to March 2021 alongside a decline in COCA cases to 46.4%. The increase in HOHA cases coincided with the second lockdown and has been investigated (1) and it was found that this peak corresponded with an increase in patients whose bacteraemia was a co- or secondary to COVID-19 in intensive care settings.

Comparing April to June 2022 to the same quarter in 2021 (April to June 2021) a slight increase was observed in HOHA cases from 30.0% to 31.9% of all cases, while the percentage of COHA cases declined slightly from 15.9% to 14.2% of all Klebsiella spp. bacteraemia cases. The number of COCA cases remained similar at 53.7% and 53.6% of all reported cases, respectively. (Figure 2c, Table S2a in the accompanying data tables).

Figure 2c. Count of Klebsiella spp. bacteraemia cases by prior trust exposure: April to June 2020, to April to June 2022

Pseudomonas aeruginosa bacteraemia

The same number of P. aeruginosa bacteraemia cases were reported in April to June 2022 and to April to June 2017 (absolute number of cases 1,015). However, a 1.4% decrease was observed in the incidence rate from 7.3 to 7.2 cases per 100,000 population, due to an absolute increase in population (Figure 3a). The count of community-onset cases were similar (from 639 to 634) but again the incidence rate decreased, by 2.1% from 4.6 to 4.5 cases per 100,000 population, respectively. Over the same period, the count and the incidence rate of hospital-onset cases increased by 1.3% from 376 to 381 cases and by 0.7% from 4.3 to 4.4 cases per 100,000 bed-days, respectively (Figure 3b, Table S3 in the accompanying data tables).

Like Klebsiella spp. cases, increases in counts and rates of hospital-onset P. aeruginosa were also observed during the second wave of the pandemic. The counts and rates of hospital-onset P. aeruginosa increased between quarters July to September 2020 and January to March 2021, to levels not seen previously seen during the entirety of the mandatory surveillance of P. aeruginosa bacteraemia. The incidence rate of hospital-onset cases peaked at 7.0 cases per 100,000 bed-days in the January to March 2021 period. The reasons for this increase have been investigated (1) and it was observed that this increase coincided with a rise in the percentage of hospital-onset bacteraemia cases who were also positive for COVID-19.

Comparing April to June 2022 with the same period in the previous year (April to June 2021), the total reported counts were similar at 1,005 and 1,015, respectively, and the rate for both quarters was 7.2 cases per 100,000 population. A 15.5% rise was observed in the hospital-onset counts which increased from 330 to 381, with a corresponding increase of 3.7% in the hospital-onset incidence rate, from 4.2 to 4.4 cases per 100,000 bed-days, respectively. Community-onset cases displayed a 6.1% decrease in both counts and rates from 675 in April to June 2021 to 634 in April to June 2022 and 4.8 to 4.5 per 100,000 population, respectively.

A comparison to the same period in 2019 (April to June 2019), which was a more typical year before the COVID-19 pandemic, shows a decrease across all categories. There was a 5.1% decline in the count of all reported cases from 1,069 to 1,015, with a corresponding decrease in rate from 7.6 to 7.2 cases per 100,000 population (Figure 3a, Table S3 in the accompanying data tables). During the same time period, counts of community-onset P. aeruginosa cases saw a similar decrease of 5.5% from 671 to 634, with a corresponding decline in the community-onset incidence rate of 5.7% from 4.8 to 4.5 per 100,000 population (see Table S3 in the accompanying data tables). There was a 4.8% decline in counts of hospital-onset P. aeruginosa cases from 398 to 381, with a decrease in the incidence rate of 4.8% from 4.6 to 4.4 per 100,000 bed-days (Figure 3b, Table S3 in the accompanying data tables). It is worth noting that the bed-days data for the current quarter is similar as it was in April to June 2019.

There is evidence of seasonality in the incidence of all-reported P. aeruginosa bacteraemia cases, with the highest rates normally observed in the July to September quarter of each financial year.

Figure 3a. Quarterly rates of all reported P. aeruginosa bacteraemia: April to June 2017, to April to June 2022

Figure 3b. Quarterly rates of hospital-onset P. aeruginosa bacteraemia: April to June 2017, to April to June 2022

Similarly, to E. coli and Klebsiella spp., COCA cases (around 50%) tend to dominate P. aeruginosa bacteraemia cases between the April to June 2020 and January to March 2022 quarters. However, in the January to March 2021 quarter, HOHA cases (48.2%) surpassed COCA cases (36.8%) for the first time since April 2020 coinciding with the peak of the second wave of the COVID-19 pandemic.

Comparing April to June 2022 to the same quarter in 2021 (April to June 2021), HOHA cases increased from 32.8% to 37.5% of all P. aeruginosa bacteraemia cases. The percentage of COHA cases decreased from 21.7% to 17.9%. COCA cases decreased from 45.2% to 44.1%. (Figure 3c, Table S3a in the accompanying data tables).

Figure 3c. Count of P. aeruginosa bacteraemia cases by prior trust exposure: April to June 2020, to April to June 2022

Epidemiological analyses of Staphylococcus aureus bacteraemia data

MRSA bacteraemia

There has been a considerable decrease in the incidence rate of all reported MRSA bacteraemia since the enhanced mandatory surveillance began in April 2007 (Figure 4a, Table S4 in the accompanying data tables). The incidence rate of all reported cases fell by 86.9% from 10.2 cases per 100,000 population in the April to June 2007 quarter to 1.3 cases per 100,000 in the April to June 2014 quarter. The rate has fluctuated between 1.0 and 1.8 since then and is currently at 1.2 cases per 100,000 population in the most recent quarter (April to June 2022).

A similar trend was observed with the incidence rate of hospital-onset cases (Figure 4b, Table S4 in the accompanying data tables). There was a steep decrease of 85.4%, from 4.9 cases per 100,000 bed-days in the April to June 2008 period to 0.8 case per 100,000 bed-days in the April to June 2014 period. Subsequently, between April to June 2014 and April to June 2022, the rate has decreased to 0.8 cases per 100,000 bed-days. Since April to June 2014, there have been fluctuations in both the number of hospital-onset infections and the hospital-onset incidence rate, ranging between 52 and 96 and 0.6 and 1.1 cases per 100,000 population, respectively.

Like Klebsiella spp. and P. aeruginosa, there was a peak in the incidence rate of hospital-onset MRSA bacteraemia, at 1.4 cases per 100,000 bed-days, in the January and March 2021 quarter (Figure 4b, Table S4 in the accompanying data tables). This was the highest rate seen for hospital-onset MRSA bacteraemia since April to June 2011. The reasons for this increase are still being investigated, although it has been observed that this increase coincided with a rise in the percentage of hospital-onset bacteraemia cases who were also positive for COVID-19.

A comparison with the same period in 2019 (April to June 2019), which was a more typical year before the COVID-19 pandemic, shows a 3.8% decrease in the total case count from 182 to 175 with a corresponding decline in the incidence rate of 4.0% from 1.3 in April to June 2019 to 1.2 cases per 100,000 population in April to June 2022 (Figure 4a, Table S4 in the accompanying data tables). Community-onset MRSA bacteraemia counts and rates also decreased by approximately 16% from 130 to 109 and 0.9 to 0.8 cases per 100,000 population (Table S4 in the accompanying data tables), respectively. Whereas the count of hospital-onset MRSA bacteraemia cases increased by 26.9% from 52 to 66, with a 26.2% increase in incidence rate from 0.6 to 0.8 per 100,000 bed-days (Figure 4b, Table S4 in the accompanying data tables).

Figure 4a. Quarterly rates of all reported MRSA bacteraemia: April to June 2007, to April to June 2022

Figure 4b. Quarterly rates of hospital-onset MRSA bacteraemia: April to June 2008, to April to June 2022

MSSA bacteraemia

Since the mandatory reporting of MSSA bacteraemia began in January 2011 there has been a general trend of increasing counts and incidence rates of cases. The count of all reported cases of MSSA bacteraemia increased by 44.2% from 2,199 to 3,172 between the January to March 2011 and April to June 2022 quarters. This was accompanied by a 34.3% increase in incidence rate from 16.8 to 22.6 per 100,000 population, respectively (Figure 5a, Table S5 in the accompanying data tables). These increases are primarily driven by increases in community-onset cases.

Between the January to March 2011 and April to June 2022 quarters, the count and the incidence rate of community-onset cases increased by 53.0% and 42.5% respectively from 1,464 to 2,240 cases and from 11.2 to 15.9 cases per 100,000 population (Table S5 in the accompanying data tables). Over the same period, the count of hospital-onset cases increased by 26.8% from 735 to 932 cases, while the hospital-onset incidence rate increased by 28.6% from 8.3 to 10.7 cases per 100,000 bed-days (Figure 5a and Figure 5b, Table S5a in the accompanying data tables).

Since the beginning of the COVID-19 pandemic, reported MSSA cases dropped to 2,754 and the rate fell to 19.6 cases per 100,000 population. However, this count and rate is still higher than at the beginning of the MSSA surveillance. This preceded a steady increase in quarterly counts up towards the end of wave 2 of the COVID-19 pandemic, quarter April to June 2021. Following this, all reported cases and rates dropped, but have been on a steady increasing trend since. Counts and rates are still exceeding quarterly counts and rates observed at the inception of MSSA surveillance.

Since the April to June 2020 quarter, there has been an increase in the incidence rate of hospital-onset MSSA bacteraemia cases. The increase in hospital-onset rate is, in part, a result of reduced hospital activity, resulting in reduced occupied overnight bed-days (Table S5 in the accompanying data tables), the denominator used for the hospital-onset rates. The increasing rate culminated in a peak during the January to March 2021 quarter, when it was 13.4 cases per 100,000 bed-days and there were 998 cases. This was the highest MSSA hospital-onset rate and count that has been observed since the inception of MSSA surveillance. This pattern is comparable to that observed in both Klebsiella spp. and P. aeruginosa.

In comparison to April to June 2019, which was during a more typical year prior to the first wave of the pandemic, there has been a 3.7% increase in the counts of all reported cases from 3,058 to 3,172 and a 3.5% increase in the rate from 21.8 to 22.6 cases per 100,000 population in the current quarter (April to June 2022). Over this same period, hospital-onset MSSA bacteraemia cases have increased by 9.7% from 849 to 932, which corresponds to a 9.1% increase in the incidence rate from 9.8 to 10.7 per 100,000 bed-days. Community-onset MSSA bacteraemia cases displayed the least change with a slight increase of 1.4% from 2,209 to 2,240, while the rates increased by 1.2% from 15.7 to 15.9 per 100,000 population over the same period.

Figure 5a. Quarterly rates of all reported MSSA bacteraemia: January to March 2011, to April to June 2022

Figure 5b. Quarterly rates of hospital-onset MSSA bacteraemia: January to March 2011 to April to June 2022

Epidemiological analyses of Clostridioides difficile infection data

Since the initiation of C. difficile infection (CDI) surveillance in April 2007, there has been an overall decrease in the count and incidence rate of both all-reported and hospital-onset cases (Figure 6a, Figure 6b and Table S6 in the accompanying data tables).

A large part of the decrease in the CDI cases and incidence rate occurred between the April to June 2007 and January to March 2012 quarters, with a 78.0% decrease in all-reported cases of CDI from 16,864 to 3,711 cases and an associated 78.8% reduction in incidence rate from 131.6 cases per 100,000 population to 27.9 cases per 100,000 population. Subsequently, between January to March 2012 and April to June 2022, the count of all-reported cases increased by 1.2% from 3,711 to 3,757 cases, however the incidence rate reduced by 4.2% from 27.9 to 26.7 cases per 100,000 population. This is, in part, due to an absolute population count increase.

There were similar, but greater, reductions among hospital-onset CDI cases with an 84.5% reduction in count of cases between April to June 2007 and January to March 2012 from 10,436 to 1,613 cases and an 83.9% reduction in the incidence rate from 112.1 to 18.1 per 100,000 bed-days. This was followed by a further 3.3% decrease in the count of cases, from 1,613 to 1,560 cases and a decrease of 0.8% in the incidence rate from 18.1 to 17.9 cases per 100,000 bed-days between January to March 2012 and April to June 2022.

When comparing the most recent quarter (April to June 2022) to April to June 2019, which is a more typical period prior to the first wave of the COVID-19 pandemic, there has been a 21.5% increase in the count of all reported cases from 3,093 to 3,757, corresponding to an 21.2% increase in the incidence rate, from 22.0 to 26.7 cases per 100,000 population (Figure 6a, Table S6 in the accompanying data tables). Community-onset CDI cases increased by 8.9% from 2,017 to 2,197 while the rate increased by 8.7% from 14.4 to 15.6 per 100,000 population (Table S6 in the accompanying data tables). Hospital-onset CDI cases increased by 45.0% from 1,076 to 1,560 which corresponds to an incidence rate increase of 44.1% from 12.4 to 17.9 cases per 100,000 bed-days (Figure 6b, Table S6 in the accompanying data tables). The reasons for these observed increases are still being investigated.

Figure 6a. Quarterly rates of all reported C. difficile: April to June 2007, to April to June 2022

Figure 6b. Quarterly rates of hospital-onset C. difficile: April to June 2007, to April to June 2022

Between the April to June 2017 and April to June 2022 quarters the largest percentage of cases were HOHA, at approximately 40% of all cases but has increased to 46% over the past 2 quarters (January to June 2022). Over the same period, the percentage of COCA cases increased from 13.4% to 28.0% and COHA cases have increased from 9.7% to 16.8% of all CDI. Community Onset Indeterminate Association (COIA) cases increased from 6.3% to 8.9% of all CDI. Much of the increase observed is likely due to improved data quality as shown by the sharp decline of cases with missing or not reported data (Figure 6c, Table S7 in the accompanying data tables).

Figure 6c. CDI rates by prior trust exposure April to June 2017, to April to June 2022

Appendix

Bed-day data

For bacteraemia and CDI, the average bed-day activity reported by acute trusts via KH03 returns is used to derive the bed-day denominator for acute trust incidence rate rates (assigned and apportioned). As of Q1 2011 to 2012, bed-day data has been available on a quarterly basis and has been used as such for Q2 2011 to 2012, to Q3 2021 to 2022.

However, UKHSA has reviewed its policy for processing KH03 data. Data irregularities identified have been flagged with colleagues at NHS England (data owners of the KH03 data set). Until we receive confirmation that any identified change in the occupied overnight bed-days for an acute trust is anomalous, UKHSA now uses the data as published in the KH03 data set. This affects all reports published since 1 December 2015 and incidence rate rates published prior that time will differ slightly as a result.

For the KH03 data used to calculate rates included in this report to be consistent over the full-time period, previously amended KH03 data for trust United Lincolnshire Hospitals (RWD) for financial year 2014 to 2015, has been altered to reflect that published in the KH03 data set. Please note that this could lead to slight differences in hospital-onset assigned rates when compared with publications prior to 1 December 2015.

KH03 data can be found on the NHS England website.

Missing data for acute trusts in the KH03 returns will continue to be processed as before, where the KH03 return for the same quarter from the previous year will be used as a proxy. The following acute trusts were thus affected:

• Moorfields Eye Hospital NHS Foundation Trust (RP6) 2007 to 2008, and 2008 to 2009 KH03 figures: replaced with 2006 to 2007 KH03 figure

• Rotherham NHS Foundation Trust (RFR): 2009 to 2010 and from April to June 2010, to April to June 2011 KH03 figures: replaced with 2008 to 2009 KH03 figure

• Sheffield Teaching Hospitals NHS Foundation Trust (RHQ) from April to June 2010, to April to June 2011 KH03 figures: replaced with 2009 to 2010 KH03 data

• The Princess Alexandra Hospital NHS Trust (RQW) April to June 2014, and October to December 2014 KH03 figures: replaced with April to June 2013, to October to December 2013 KH03 figures, respectively

• Ipswich Hospital NHS Trust (RGQ) January to March 2016 KH03 figure: replaced with January to March 2015 figures

• West Suffolk NHS Foundation Trust (RGR) April to June 2016, to October to December 2016 and April to June 2017 KH03 figures: replaced with April to June 2015, to October to December 2015 KH03 figures

• Gloucestershire Hospitals NHS Foundation Trust (RTE) October to December 2016, to January to March 2017 KH03 figures: replaced with October to December 2015, to January to March 2016 KH03 figures

The KH03 data used for this report was published on 23 August 2022. This may include revisions of previously published KH03 data used in earlier reports.

Population data

National incidence rates are calculated using 2007 to 2020 mid-year resident population estimates which are based on the 2011 census for England (2021 and 2022 estimates are based on 2020 mid-year estimates).

Definitions

Bacteraemia hospital-onset (trust-apportioned) cases

Include patients who are (i) in-patients, day-patients, emergency assessment patients or not known, and (ii) have had their specimen taken at an acute trust or not known, and (iii) specimen was taken on or after day 3 of the admission (admission date is considered day ‘one’). Cases that do not meet these criteria are categorised as community-onset (not-trust apportioned).

CDI hospital-onset (trust-apportioned) cases

Include patients who are (i) in-patients, day-patients, emergency assessment patients or not known, and (ii) have had their specimen taken at an acute trust or not known, and (iii) specimen was taken on or after day 4 of the admission (admission date is considered day ‘one’). Cases that do not meet these criteria are categorised as community-onset (not-trust apportioned).

Historically, report published before September 2017 have used the term ‘trust- apportioned’ to describe cases meeting the above conditions for apportionment and ‘not trust-apportioned’ for those that do not. Moving forward, these terminologies have been updated to ‘hospital-onset’ and ‘community-onset’ respectively. Please note that this is simply a change in terminology and does not constitute a change in the methodology for apportionment.

Prior trust exposure

From April 2017, reporting trusts were asked to provide information on whether patients with CDI had been admitted to the reporting trust within the 3 months prior to the onset of the current case. This allows a greater granulation of the healthcare association of cases. This was extended to all other data collections in 2019.

Cases are split into one of 6 groups for CDI and 5 groups for the bacteraemias:

CDI prior trust exposure categories

1. Hospital-onset healthcare-associated: date of onset is greater than 2 days after admission (where day of admission is day 1).
2. Community-onset healthcare-associated: is not categorised HOHA and the patient was most recently discharged from the same reporting trust in the 28 days prior to the specimen date (where day 1 is the specimen date).
3. Community-onset indeterminate association: is not categorised HOHA and the patient was most recently discharged from the same reporting trust between 29 and 84 days prior to the specimen date (where day 1 is the specimen date).
4. Community-onset community-associated: is not categorised HOHA and the patient has not been discharged from the same reporting organisation in the 84 days prior to the specimen date (where day 1 is the specimen date)
5. Unknown: the reporting trust answered ‘Don’t know’ to the question regarding previous discharge in the 3 months prior to CDI case.
6. No Information: the reporting trust did not provide any answer for questions on prior admission.

Bacteraemia prior trust exposure categories

In addition, in April 2020, the HCAI DCS has included questions relating to prior trust exposure to the same acute trust reporting Gram-negative bacteraemia cases. These additional mandatory items were developed to assist the UK governments ambition to reduce healthcare-associated Gram-negative BSI and CDI from a 2019 baseline to threshold levels. This supports the intention to reduce Gram-negative BSI by 25% by March 2022, and by 50% by March 2024.

Cases since April 2020 have also been categorised as:

1. Hospital-onset healthcare-associated: date of onset is greater than 2 days after admission (where day of admission is day 1).
2. Community-onset healthcare-associated: is not categorised HOHA and the patient was most recently discharged from the same reporting trust in the 28 days prior to the specimen date (where day 1 is the specimen date).
3. Community-Onset, Community Associated: is not categorised HOHA and the patient has not been discharged from the same reporting organisation in the 28 days prior to the specimen date (where day 1 is the specimen date).
4. Unknown: the reporting trust answered ‘Don’t know’ to the question regarding previous discharge in the month prior to the current episode.
5. No Information: the reporting trust did not provide any answer for questions on prior admission.

Total reported cases

This is the total count of infections for each organism as of the date of extraction. Please note that for C. difficile, this count excludes those from patients less than 2 years old.

Episode duration

The length of an infection episode is defined as 14 days (28 days for CDI) from the earliest case’s specimen date (day ‘one’).

Incidence rate calculations

MRSA, MSSA and E. coli, Klebsiella spp., P. aeruginosa bacteraemia, and CDI population incidence rate (episodes per 100,000)

This incidence rate is calculated using the number of episodes and the mid-year population for England:

That is: the number of episodes is multiplied by 100,000, then multiplied by the number of days in the year, then divided by the mid-year of population for the same year for England, then divided by the number of days in the quarter.

MRSA, MSSA and E. coli, Klebsiella spp., P. aeruginosa and CDI hospital-onset incidence

This incidence rate is calculated using the number of episodes and the KH03 average bed-day activity (see bed-day data above) and is calculated as follows:

That is: the number of episodes is multiplied by 100,000, then divided by the average number of beds occupied-overnight in a quarter, then divided by the number of days in the same quarter.

Graphs and percentage change calculation

Please note that percentage changes in rate have been calculated using raw rate figures while those presented in the tables and commentary have been rounded to one decimal place. Similarly, graphs included in this report were plotted using raw rates figures. The raw rate figures are included in the Quarterly Epidemiological Commentary’s accompanying data.

Quarters

In publications prior to March 2016, all references to quarterly data are based on calendar year definitions and not financial year definitions, that is:

• Q1 2014: January to March 2014
• Q2 2014: April to June 2014
• Q3 2014: July to September 2014
• Q4 2014: October to December 2014

However, for all subsequent publications, including this one, all references to quarterly data are based on financial year definitions and not calendar year definitions, that is:

• Q1 2014 to 2015: April to June 2014
• Q2 2014 to 2015: July to September 2014
• Q3 2014 to 2015: October to December 2014
• Q4 2014 to 2015: January to March 2015

References

1. Sloot R, Nsonwu O, Chudasama D, Rooney G, Pearson C, Choi H, Mason E, Springer A, Gerver S, Brown C, Hope R. ‘Rising rates of hospital-onset Klebsiella spp. and Pseudomonas aeruginosa bacteraemia in NHS acute trusts in England: a review of national surveillance data.’ August 2020 to February 2021. Journal of Hospital Infection 2021: September 2020

Enquiries and feedback

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